However, his strong support of Archbishop Laud, and his toughness on Puritans, led to his being
imprisoned in the Tower of London by the Parliamentarian
faction from 1641 to 1659. Unlike Laud, he survived, and was
allowed the freedom to write notes on improvements to the Book of
Common Prayer, on which he later had some influence.

While in the Tower, he vowed to devote a sum of money to "some
holy and pious employment" should he be released. To fulfil this
vow, he chose to pay for a new Chapel for Pembroke College, and had
it built by his nephew Christopher Wren — one of his first
buildings, consecrated in 1665. Matthew Wren also led the movement
to rebuild St Paul's Cathedral after it had
been damaged by the Puritans, and again his nephew accomplished the
task.